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Wikipedia reports: “For many years, there has been a large debate as to whether Purgatorius is a primitive member of the Primates or a basal member of thePlesiadapiforms.” Here (Fig. 1) taxa from the Plesiadapiformes have giant procumbent (rat-like) incisors followed by a long diastema, followed by flat molars…completely UNLIKE Purgatorius. So what were they thinking?

Halliday et al. 2015
nested Purgatorius outside crown group placentals with Protunugulatum (Fig 1). That seems reasonable, though it is twice the size. However, the large reptile tree (LRT, 1044 taxa) was not able to replicate most of the Halliday team’s cladogram, which nested hyraxes with elephant shrews…and horses… and that clade with pre-odontocetes and an early artiodactyl. It just gets worse after that. Protunugulatum was originally allied with condylarths, large plant-eating mammals. Halliday et al. nested it outside the placentals. Wible et al. 2007 nested it with whales + artiodactyls (a clade not validated by the LRT).

Purgatorius is another one of those fossilsknown from an incompleted mandible with teeth and little else. Based on a lack of other bones, this is the sort of fossil the LRT cannot successfully resolve and it does not make it onto the list. So we go to plan #2: visual comparisons.

Figure 1. Purgatorius compared to other basal and often Paleocene mammals. Given these choices, Purgatorius looks more like Palaechthon, the basal dermopteran, than any other taxa in the LRT. Taxa in yellow nest together in the LRT with primates. Taxa in pink nest with rats and rabbits. Maelestes is a basal tenrec.

Rat-sized Purgatorius unio
(Valen and Sloan 1965; Latest Cretaceous/Earliest Paleocene) gained some early notoriety as the earliest known primate. Ankle bones found in association with Purgatorius, but not articulation, show signs of being flexible like those of primates (Kaplan 2012).

I can describe Purgatorius in the simplest of terms
based on comparisons to related basal mammal taxa (Fig. 1) and without describing any molar cusps (except one).

small in overall size (skull < 2cm in length)

robust mandible with convex dorsal and ventral rims and straight in occlusal view

incisors likely procumbent, but not large

canine tiny

three robust premolars and three robust molars with one very tall cusp

Premolar #3 taller than other teeth

Based on a visual comparison
of candidate taxa (Fig. 1), Purgatorius looks more like Protungulatum and even more like Palaechthon. The latter nests with flying lemurs like Cynocephalus. So we’re close to the base of primates, but closer to their cousins, and far from plesiadapiformes.

there are a few more I’m overlooking. I’ll add them as they come to me.

Figure 1. Glires and Euarchonta are two clades within the Mammalia in the LRT.

Let’s focus on PlesiadapiformesBloch et al. 2007 found plesiadapiforms (Plesiadapis, Carpolestes and kin) more closely related to primates than to any other group. They did not test against rodents and multituberculates. The LRT does not replicate these results, but finds plesiadapiforms more closely related to multituberculates and rodents when included.

According to Bloch & Boyer 2002“Plesiadapiforms share some traits with living primates, including long fingers well designed for grasping, and other features of the skeleton that are related to arboreality.” That’s fine, but there are other taxa in the tree topology with long fingers, too.

ParomomyidaeKrause 1991 reports, “Paromomyids …have long been regarded by most workers as members of the Plesiadapiformes.” Again, the LRT does not support this, but nests Paromomyids, like Ignacius (Fig. 2), with rodents, like Mus and Paramys. Paromomyids have squared off and flat molars, but Paromomys does not.

Figure 2. The skull of Ignacius nests with other rodents, not plesiadapiformes. Ironically it is closer to the squirrel-like Paramys than to Paromomys.

Beard 1990 thought paromomyids,
as plesiadapiforms, where close to colugos or “flying lemurs”. The LRT (Fig. 1) does not support this relationship. Rather paromomyids, like Ignacius, were squirrel-like, able to scamper both in the trees and on the ground. Ignacius graybullianus (USNM 421608, Fig. 1) is a new taxon that nests as a basal rodent in the LRT.

Figure 3. Ignacius clarkforkensis known parts.

Remmber, no primates
have giant anterior dentary teeth. The aye-aye,Daubentonia, has such teeth, but the LRT finds it nests with Plesiadapis and multituberculates and rodents, not primates. Yes, plesiadapiformes and Ignacius had long limbs, big brains and binocular vision, but by convergence with primates.

Figure 2. My daughter Stephanie one week before giving birth to grandson James (nickname: Jet) and about three years ago.

Being a mom goes way, way backIn our lineage, first cells stuck together, flagella out (Fig. 3). Then four cells stuck together. Then eight. Ultimately hundreds stuck together creating a sphere, or blastula. And little blastulas formed inside until they were large enough to break free.

Figure 3. Blastula from the book, “From the Beginning” by Peters 1991.

Plesiosaurs and primates capable of understanding prehistory
followed shortly thereafter. The basics of being a mother haven’t really changed much in the last few billion years.

From the Franzen et al. 2009 conclusion:“Darwinius masillae represents the most complete fossil primate ever found, including both skeleton, soft body outline and contents of the digestive tract. Study of all these features allows a fairly complete reconstruction of life history, locomotion, and diet. Any future study of Eocene-Oligocene primates should benefit from information preserved in the Darwinius holotype. Of particular importance to phylogenetic studies, the absence of a toilet claw and a toothcomb demonstrates that Darwinius masillae is not simply a fossil lemur, but part of a larger group of primates, Adapoidea, representative of the early haplorhine diversification.”

In a published comment Beard 2009 wrote:“Unbridled hoopla attended the unveiling of a 47-million-year-old fossil primate skeletonat the American Museum of Natural History in New York on 19 May. Found by private collectors in 1983 in Messel, Germany, the press immediately hailed the specimen as a “missing link” and even the “eighth wonder of the world.”

“Overall proportions and anatomy resemble that of a lemur, and the same is true for other adapiform primates. A new genus and species of adapiform primate, Darwinius masillae(Franzen et al., 2009; Eocene, 50 mya ). The adapids are a branch of the primate tree that leads to modern lemurs. Ida would have to have anthropoid-like features that evolved after anthropoids split away from lemurs and other early primates. Here, alas, Ida fails miserably.” The reasons for that “fail” were not listed in the Beard note.

Taxon exclusion?The large reptile tree, (LRT, 896 taxa), currently tests only a few primates. At this stage, Darwinius does indeed nest at the base of higher primates (simians), alongside Tarsius, the extant tarsier, but there are many dozen primate taxa that have not been included in the LRT.

Figure 1. Darwinius overall plus an X-ray showing the transition from milk teeth to adult teeth in this juvenile specimen.

In the LRT,
nesting only a few primates at present, the adapid prosimian,Notharctus, is basal to higher primates including humans (genus Homo). Tarsius, the tarsier, nests between Notharctus and Proconsul, a basal anthropoid (ape). Darwinius nests with Tarsius, but lacks the many specialized autapomorphies that characterize extant tarsiers like:

oversized eyes

distally fused tibiafibula

elongated pedal digits 4 and 5.

hyperelongated astragalus and calcaneum

cervicals insert further beneath the skull

Figure 2. Tarsius, the extant tarsier. Note the several autapomorphies displayed here vs. the many plesiamorphies in Darwinius.

Wikipedia reports“Most experts hold that the higher primates (simians) evolved from Tarsiidae, branching off the Strepsirrhini before the appearance of the Adapiformes.”If true, Darwinius is close to the lineage of humans. “A smaller group agrees with Franzen et al. that the higher primates descend from Adapiformes (Adapoidea). The view of paleontologist Tim White is that Darwinius is unlikely to end the argument.”

NBC news reports,here that “Ida is as far removed from the monkey-ape-human ancestry as a primate could be, says Erik Seiffert of Stony Brook University in New York. The new analysis says Darwinius does not belong in the same primate category as monkeys, apes and humans. Instead, the analysis concluded, it falls into the other major grouping, which includes lemurs.”

Nature reports on the “media frenzy”here in a paper entitled: “A hyped-up fossil find highlights the potential dangers of publicity machines. To be fair, the authors’ claims at the press conference were appropriately measured. Nonetheless, the researchers were fully involved in the documentaries and the media campaign, which associate them with a drastic misrepresentation of their research.”

“Another damaging aspect of the events was the unavailability of the paper ahead of the press conference and initial media coverage. This prevented scientists other than those in the team from assessing the work and thereby ensuring that journalists could give a balanced account of the research.

“There is no reason to think that PLoS ONE’s editors and reviewers did less than their duty to the paper. Nonetheless, the clock was ticking at the time of submission.”

“In principle, there is no reason why science should not be accompanied by highly proactive publicity machines. But in practice, such arrangements introduce conflicting incentives that can all too easily undermine the process of the assessment and communication of science.”

The primate experts can hash this out.
At present, with so few primates tested, Darwinius is still a candidate to be at the transition from prosimian to simian in the LRT, as it presently nests… until additional taxa knock it out.

Added within minutes of posting
I ran across this reference:Gingerich PD et al. 2010.Darwinius masillae is a Haplorhine — Reply to Williams et al. (2010). Journal of Human Evolution. 59(5)574-576 where they report, “Williams et al. (2010) imply that ‘total evidence’ means study of hundreds of characters in a great many taxa. However, total evidence is about combining data before analysis and not about the size of the resulting matrix. “We agree with Seiffert et al., 2009 and Williams et al., 2010, and others that there is a strepsirrhine–haplorhine dichotomy in primate evolution. We employ the same cladistic methods. We accept that total evidence drawn from many sources is advantageous. Why then do we reach such a different conclusion about the systematic position of Darwinius? Given that our methods are the same, then our contrasting results can only be explained by differences in the number and balance of taxa chosen for study, the character matrix used to analyze higher-level primate phylogeny, the outgroup chosen to root a phylogenetic network, or some combination of these.”More details on their arguments are found here.

Figure 1. Daubentonia was considered a primate for over 150 years. Here it nests with Plesiadapis, rodents and rabbits. It’s the only living plesiadapid.

According tothe AMNH website on Sir Richard Owen and the Aye-Aye, “For the first 100 years after the first aye-aye was brought to Europe in the 1780s, debate swirled over whether it was a rodent, a primate, or most closely related to a kangaroo.

“The root of this confusion lay in the aye-aye’s odd collection of behavioral and morphological traits that make it appear to be composed of spare parts of other animals: continuously growing front teeth, batlike ears, a foxlike tail, abdominal mammary glands, claws on most digits, and spindly, dexterous middle fingers.

“It uses its middle finger to tap along a branch and moves its ears forward and back to help locate hollow channels within the wood created by wood-boring insect larvae. Once it detects a channel, the aye-aye uses its specialized front teeth to pry open the wood and then inserts one of its fingers to extract the larvae.”

The AMNHhas been wrong before. And that’s okay. This is Science. We can fix mistakes. Tradition should never trump testing. If you’re not sure where a taxon should nest, if it is constantly described as weird or autapomorphic, you simply need to test your ‘ugly duckling‘ taxon against a larger gamut of candidates. You’ll probably find your taxon is not so weird after all, when compared to its true sisters. Daubentonia has ‘rodent-like’ teeth because it is more closely related to rodents. It’s as simple as that. And convergence happens.

Figure 2. Skeleton of Daubentonia (aye-aye). Like other plesiadapids, it convergences with the lemuroid primates.

According to the AMNH, Owen’s 1863 descriptionput arguments about the aye-aye’s taxonomy to rest as it focused “attention away from the striking unusual characteristics, like the continuously growing teeth, and toward primate-like characteristics such as forward-facing eyes and an opposable thumb, providing firm evidence for why the aye-aye should be classified as a primate.”

In the large reptile tree
(LRT), we don’t focus attention toward or away from anything. We score all the traits evenly and let PAUP figure out which taxa any new taxa nests most closely to. In this test, Daubentonia (Gmelin 1788. Geoffroy Saint-Hillaire 1795; 40 cm snout-vent length; extant) nested most closely with Plesiadapis within the clade Glires. The ever-growing teeth are traits inherited from a basal member of Glires. Only the hallux has a nail. The rest of the toes bear claws. The rest of the primate-like traits are convergent, probably due to its arboreal niche.

Discovered in 1780by French zoologist, LJM Daubenton, it was originally identified as a squirrel (Gmelin 1788) and named Sciurus madagascariensis. Geoffrey Saint-Hilaire (1795) provided a new generic name. Daubentonia was first considered a primate by Schreber 1800 who renamed it Lemur psilodactylus, a name now considered an invalid junior synonym. More taxonomic misadventures can be found here.

Figure 3. Two clades within the Mammalia from the LRT. Here Daubentonia nests with Plesiadapis, both far from primates.

This is the yet another‘rodent-like’ mammal that actually nests with rodents. Other similar originally mis-nested Glires we’ve already covered include:

They all have big incisors.
A few, like Daubentonia and Tupaia, have a complete postorbital ring. The wide jugals of Plesiadapis and Taeniolabis, provide forward-oriented eyes, just like their sister, Daubentonia.

More taxonomic issuesaccording to Yoder et al. 1996.“Morphological studies of Daubentonia have been less consistent in their conclusions, finding the aye-aye to be either a highly derived member of the Malagasy primate family Indridae (Schwartz 1986), the basal-most branch of the strepsirrhines (Groves 1990), or unclassifiable in relation to other living primates (Oxnard 1981).”

according to Picone and Sineo 2012.“Both MP and BI topologies show Daubentonia as an independent monophyletic lineage, sister group of all other Strepsirhini.”(= Prosiminiii or lemurs). You should know, BTW, they tested only lemurs with Tupaia as the outgroup and Daubentonia nested between them, just like the LRT without all the taxon exclusion. A priori taxon exclusion is… once again… the main problem here.

Figure 1. Carpolestes has a thumb-like hallux and polled (digit 1 on manus and pes). Those are primitive traits, not derived ones in this rabbit sister.

In their paper on primate origins, Bloch and Boyer 2006 report,“Extant primates are distinct from other eutherian mammals in having large brains, enhanced vision brought about in part by optical convergence, the ability to leap, nails on at least the first toes, and grasping hands and feet.”

In the LRTthe basalmost placental, Monodelphis domestics (which does not have a pouch), the forward facing eyes have a degree of optical convergence, adults pounce on their prey and they hold down with their forefeet, which, alas, do not appear to have nails. But 3 out of 4 is coming along way…

Figure 3. The marsupial, Monodelphis domestica, nests as the oldest known placental. Females do not have a pouch, but epipubes are retained.

Bloch and Boyer 2006 report,“Plesiadapiformes has long been considered an archaic radiation of primates. Evidence in favor of a plesiadapiform-euprimate link was based largely on dental and postcranial similarities, whereas the absence of a postorbital bar and other cranial features in certain plesiadapiforms provided evidence against this hypothesis. An alternative hypothesis, that Plesiadapiformes share a closer relationship to extant flying lemurs (Dermoptera) than to Euprimates, has been strongly challenged and is not followed here.”

Unfortunately, Bloch and Boyer
do not consider the third alternative, the one recovered in the LRT with a plesiadapiform relationship to rabbits, not primates. Like little kangaroos, rabbits also originated in the trees.

The large reptile tree
(LRT) nests two plesiadapiformes, Carpolestes (Fig. 1) and Plesiadapis (Fig. 2), with rabbits, like Gomphos (Fig. 3), within the clade Glires, far from primates like Nothrarctus, which developed nails by convergence. When rabbits left the trees, they lost their hallux and pollex.

In the LRT,
primates arise from a sister to the tree shrews Ptilocercus near the base of the Triassic/Jurassic placental radiation. By contrast, plesiadapidformes arise from a sister to Henkelotherium and the more rabbit-like tree shrew, Tupaia. These taxa share long, procumbent lower incisors and a long diastema. Tupaia has a circumorbital ring, but other Glires do not.

The Bloch and Boyer published cladogramincluded only 9 taxa and no rabbits.

Bloch and Boyer report,“Several adaptive scenarios have been proposed to explain these [primate] specializations: (i) “grasp-leaping” locomotion (3), which predicts simultaneous evolution of grasping and leaping; (ii) visually directed predation (4), which predicts simultaneous evolution of forward-facing orbits and grasping; and (iii) terminal branch feeding on nectar and flowers, which allows that grasping evolved independently of other traits. The lack of well-preserved skulls and skeletons of the earliest primates has precluded testing of these hypotheses.”

Bloch and Boyer are overlookingthe living breathing, leaping and grasping basal primate, Ptilocercus (Fig. 4), or the basalmost placental, Monodelphis (Figs. 1,2) have most if not all of these morphological and behavioral traits. So… thumbs are primitive! Derived taxa, like whales and hoofed ungulates, tend to lose them.

Figure 4. Ptilocercus in vivo, holding prey with its small hands while eating it.

Note added July 31, 2016:The addition of more taxa preserves the close relationship of pangolins to primates,

At present, the large reptile tree (LRT) includes very few mammalsso keep that in mind. The LRT (now at 704 taxa) is also not fine tuned to mammal traits, like molar shapes, so keep that in mind.

So here it is:
the large reptile tree nests the pangolin, Manis, with the basal lemur, Notharctus. And Notharctus is derived from basal carnivores like Vulpavus.

Pangolins have been difficult to nest.
Recent DNA tests (Murphy et al. 2001, Beck et al. 2006) nested pangolins with carnivores, but could be no more specific than that because fossil taxa cannot be tested for DNA.

Figure 1. Therapsida includes the pangolin, Manis, which nests here with Notharctus. one of only a few mammals tested so far.

Here’s the early morphological evidencelinking Manis to Notharctus using traits that are NOT in the LRT.

Flexible vertebral column – pangolins use to roll up, lemurs use to wind up then jump from tree to tree and land without a jolt

There are several traits
in the LRT that pangolins share with people to the exclusion of lemurs, all by convergence, so not worth going into.

Some atavisms (genetic reversals) in Manis
that most other mammals don’t have include the following:

Chevrons

Scales

Low to absent coronoid process

Elongate caudal transverse processes

The important thing here
is that given the opportunity to nest with the basal carnivores, Vulpavus,Nandinia and Chriacus, Manis nested instead with Notharctus.

Keratin scalesWhat opossums and rats have on their tails, pangolins have all over their bodies.

The order of the loss of facial bones
provides clues to the chronology of evolutionary events in pangolins. The loss of the lateral temporal bar (posterior jugal + squamosal) occurred in all pangolins, but the loss of the jugal is apparent in ground forms, so this was a trees down order, with burrowing following tree climbing. The clavicle is also lost in pangolins.

Diet: ants and termites.
So this is what happens when a lemur changes diet and becomes solitary, and depends on sense of smell, rather than sight. Elongate tongue is convergent with that of chameleons, woodpeckers, anteaters and nectar bats. Some pangolins burrow. Loss of the lower temporal bar and loss of most of the jugal in some species goes along with loss of the coronoid process in this anteater. Manis doesn’t need chomping muscles. Nor does it need speed and leaping ability. Given an ant diet and solitary social life, perhaps that makes it easier to visualize how Manis could be derived from a more active, social lemur-like ancestor.